Re: Residue Charges

From: Ajasja Ljubetič (ajasja.ljubetic_at_gmail.com)
Date: Fri Mar 02 2018 - 08:55:31 CST

And you can retrieve the charges in VMD using:

$sel get charge (link to manual
<http://www.ks.uiuc.edu/Research/vmd/vmd-1.7.1/ug/node79.html#table:ug:keywords>),
where sel is the atomselection for the atoms that you are interested in.

Best,
Ajasja

On 2 March 2018 at 15:49, Sharp, Kim <sharpk_at_pennmedicine.upenn.edu> wrote:

> the charge on each atom is specified in the topology file(s) that you
> used to build the system- they are stored in the *.psf file, and they do
> not change during the simulation, which is why they don't need to be
> written to the dcd file.
>
>
> On 03/02/2018 09:35 AM, Alex Saad-Falcon wrote:
> > In each frame of a .dcd file, the positions of all the atoms are
> > available. I would also like to know the formal charge each atom has.
> > Online, it is possible to find typical charges for residues under
> > certain conditions such as pH. However, it would be better to pull the
> > charge of each residue from NAMD somehow. Does anyone know how?
> >
> > Thanks,
> >
> > Alex
>
> --
> Kim Sharp, Ph.D,
> Dept. of Biochemistry & Biophysics
> Chair, Biochemistry & Molecular Biophysics Graduate Group
> Perelman School of Medicine at the University of Pennsylvania
> 805A Stellar Chance
> Philadelphia, PA 19104
> webpage: crystal.med.upenn.edu
> 215-573-3506
>
>

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